Identification and analysis of polyserine linker domains in prokaryotic proteins with emphasis on the marine bacterium Microbulbifer degradans

Protein Science

Volumn 13, Issue 5, 2004, Pages 1422-1425

  Howard, Michael B ^a   Ekborg, Nathan A ^a   Taylor, Larry E ^a   Hutcheson, Steven W ^a   Weiner, Ronald M ^a  

^a UNIVERSITY OF MARYLAND   (United States)

Author keywords

Domain linkers; Extracellular depolymerases; Marine bacterium 2 40; Microbulbifer degradans; Polyserine linker; Secreted carbohydrases

Indexed keywords

BACTERIAL PROTEIN; CARBOHYDRATE; LIPOPROTEIN; POLYPEPTIDE; SERINE;

ACYLATION; AMINO ACID SEQUENCE; AMINO TERMINAL SEQUENCE; ARTICLE; BACTERIOPLANKTON; CARBOHYDRATE METABOLISM; CONTROLLED STUDY; ENZYME ACTIVE SITE; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROKARYOTE; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN DOMAIN;

ALTEROMONADACEAE; AMINO ACID SEQUENCE; BACTERIAL PROTEINS; CELLULASE; MOLECULAR SEQUENCE DATA; OCEANS AND SEAS; PEPTIDES; PROTEIN STRUCTURE, TERTIARY;

BACTERIA (MICROORGANISMS); BACTERIUM 2-40; EUKARYOTA; MICROBULBIFER; MICROBULBIFER DEGRADANS; PROKARYOTA; UNCULTURED MARINE BACTERIUM;

EID: 1942440973     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1110/ps.03511604     Document Type: Article

References (28)

1. Anderson, T.A., Levitt, D.G., and Banaszak, L.J. 1998. The structural basis of lipid interactions in lipovitellin, a soluble lipoprotein. Structure 6: 895-909.
2. Andrykovich, G. and Marx, I. 1988. Isolation of a new polysaccharide digesting bacterium from a salt marsh. Appl. Microbiol. Biotechnol. 54: 1061-1062.
3. Beguin, P. and Aubert, J.P. 1994. The biological degradation of cellulose. FEMS Microbiol. Rev. 13: 25-58.
4. Bhandari, D.G., Levine, B.A., Trayer, I.P., and Yeadon, M.E. 1986. 1H-NMR study of mobility and conformational constraints within the proline-rich N-terminal of the LC1 alkali light chain of skeletal myosin. Correlation with similar segments in other protein systems. Eur. J. Biochem. 160: 349-356.
5. Black, G.W., Rixon, J.E., Clarke, J.H., Hazlewood, G.P., Theodorou, M.K., Morris, P., and Gilbert, H.J. 1996. Evidence that linker sequences and cellulose-binding domains enhance the activity of hemicellulases against complex substrates. Biochem. J. 319: 515-520.
6. Brown, I.E., Mallen, M.H., Charnock, S.J., Davies, G.J., and Black, G.W. 2001. Pectate lyase 10A from Pseudomonas cellulosa is a modular enzyme containing a family 2a carbohydrate-binding module. Biochem. J. 355: 155-165.
7. Burton, J., Wood, S.G., Pedyczak, A., and Siemion, I.Z. 1989. Conformational preferences of sequential fragments of the hinge region of human IgA1 immunoglobulin molecule: II. Biophys. Chem. 33: 39-45.
8. Ferreira, L.M., Durrant, A.J., Hall, J., Hazlewood, G.P., and Gilbert, H.J. 1990. Spatial separation of protein domains is not necessary for catalytic activity or substrate binding in a xylanase. Biochem. J. 269: 261-264.
9. Garcia-Vallve, S., Romeu, A., and Palau, J. 2000. Horizontal gene transfer of glycosyl hydrolases of the rumen fungi. Mol. Biol. Evol. 17: 352-361.
10. Gilkes, N.R., Warren, R.A., Miller Jr., R.C., and Kilburn, D.G. 1988. Precise excision of the cellulose binding domains from two Cellulomonas fimi cellulases by a homologous protease and the effect on catalysis. J. Biol. Chem. 263: 10401-10407.
11. Gilkes, N.R., Henrissat, B., Kilburn, D.G., Miller Jr., R.C., and Warren, R.A. 1991. Domains in microbial β-1, 4-glycanases: Sequence conservation, function, and enzyme families. Microbiol. Rev. 55: 303-315.
12. Gonzalez, J. and Weiner, R. 2000. Phylogenetic characterization of a marine bacterium strain 2-40, a degrader of complex polysaccharides. Int. J. Syst. Bacteriol. 8: 831-834.
13. Hall, J., Hazlewood, G.P., Huskisson, N.S., Durrant, A.J., and Gilbert, H.J. 1989. Conserved serine-rich sequences in xylanase and cellulase from Pseudomonas fluorescens subspecies cellulosa: Internal signal sequence and unusual protein processing. Mol. Microbiol. 3: 1211-1219.
14. Howard, M.B., Ekborg, N.A., Taylor, L.E., Weiner, R.M., and Hutcheson, S.W. 2003. Genomic analysis and initial characterization of the chitinolytic system of Microbulbifer degradans strain 2-40. J. Bacteriol. 185: 3352-3360.
15. Kellett, L.E., Poole, D.M., Ferreira, L.M., Durrant, A.J., Hazlewood, G.P., and Gilbert, H.J. 1990. Xylanase B and an arabinofuranosidase from Pseudomonas fluorescens subsp. cellulosa contain identical cellulose-binding domains and are encoded by adjacent genes. Biochem. J. 272: 369-376.
16. Knowles, J., Lehtovaara, P., Penttila, M., Teeri, T., Harkki, A., and Salovuori, I. 1987. The cellulase genes of Trichoderma. Antonie Van Leeuwenhoek 53: 335-341.
17. Krieger, F., Fierz, B., Bieri, O., Drewello, M., and Kiefhaber, T. 2003. Dynamics of unfolded polypeptide chains as model for the earliest steps in protein folding. J. Mol. Biol. 332: 265-274.
18. Ladurner, A.G. and Fersht, A.R. 1997. Glutamine, alanine or glycine repeats inserted into the loop of a protein have minimal effects on stability and folding rates. J. Mol. Biol. 273: 330-337.
19. Liu, J. and Rost, B. 2003. NORSp: Predictions of long regions without regular secondary structure. Nucleic Acids Res. 31: 3833-3835.
20. Madan Babu, M., and Sankaran, K. 2002. DOLOP-database of bacterial lipoproteins. Bioinformatics 18: 641-643.
21. McKie, V.A., Vincken, J.P., Voragen, A.G., van den Broek, L.A., Stimson, E., and Gilbert, H.J. 2001. A new family of rhamnogalacturonan lyases contains an enzyme that binds to cellulose. Biochem. J. 355: 167-177.
22. Millward-Sadler, S.J., Davidson, K., Hazlewood, G.P., Black, G.W., Gilbert, H.J., and Clarke, J.H. 1995. Novel cellulose-binding domains, NodB homologues and conserved modular architecture in xylanases from the aerobic soil bacteria Pseudomonas fluorescens subsp. cellulosa and Cellvibrio mixtus. Biochem. J. 312 (Pt. 1): 39-48.
23. Netherwood, T., Bowden, R., Harrison, P., O'Donnell, A.G., Parker, D.S., and Gilbert, H.J. 1999. Gene transfer in the gastrointestinal tract. Appl. Environ. Microbiol. 65: 5139-5141.
24. Radford, S.E., Laue, E.D., Perham, R.N., Martin, S.R., and Appella, E. 1989. Conformational flexibility and folding of synthetic peptides representing an interdomain segment of polypeptide chain in the pyruvate dehydrogenase multienzyme complex of Escherichia coli. J. Biol. Chem. 264: 767-775.
25. Rixon, J.E., Clarke, J.H., Hazlewood, G.P., Hoyland, R.W., McCarthy, A.J., and Gilbert, H.J. 1996. Do the non-catalytic polysaccharide-binding domains and linker regions enhance the biobleaching properties of modular xylanases? Appl. Microbiol. Biotechnol. 46: 514-520.
26. Shen, H., Schmuck, M., Pilz, I., Gilkes, N.R., Kilburn, D.G., Miller Jr., R.C., and Warren, R.A. 1991. Deletion of the linker connecting the catalytic and cellulose-binding domains of endoglucanase A (CenA) of Cellulomonas fimi alters its conformation and catalytic activity. J. Biol. Chem. 266: 11335-11340.
27. Tomme, P., Van Tilbeurgh, H., Pettersson, G., Van Damme, J., Vandekerckhove, J., Knowles, J., Teeri, T., and Claeyssens, M. 1988. Studies of the cellulolytic system of Trichoderma reesei QM 9414. Analysis of domain function in two cellobiohydrolases by limited proteolysis. Eur. J. Biochem. 170: 575-581.
28. Warren, R.A., Beck, C.F., Gilkes, N.R., Kilburn, D.G., Langsford, M.L., Miller Jr., R.C., O'Neill, G.P., Scheufens, M., and Wong, W.K. 1986. Sequence conservation and region shuffling in an endoglucanase and an exoglucanase from Cellulomonasfimi. Proteins 1: 335-341.